Debugging BindFlow runs

Debugging BindFlow runs#

To troubleshoot a BindFlow run:

  1. Check the main log file

    • Located in the .snakemake directory of the running simulation.

    • Search for the keyword error.

    • Note the rule name and job ID associated with the failure.

  2. If running on an HPC system

    • Go to the slurm_logs directory.

    • Find the corresponding .err and/or .out files using the rule name and job ID.

    • Review their contents — in most cases this will clearly indicate what went wrong and which steps were involved.

  3. If the issue remains unclear

    • Return to the main log file and locate the reported working directory.

    • Explore that directory for more detailed logs.

    • For GROMACS simulations, check for .log and .lis files in the specified directory.